Hello,
I do not understand why you have to deploy it manually then there is a implemented mechanism in NWDI about moving your changes trough the landscape.
Of course extracting the .ear and deploy it with SDM or even TELNET will work.
However I wonder why you have not used CM Services based on Activities. It would have given you the flexibility (due to you have been forced to make all these gymnastics)
If you want to be sure you will have the latest version you might
1. create a dummy change (f.a. add a comment)
2. check in ,release and activate this activity.
3. make a try to transport it through DEV to TEST to PROD.
Then this should be the latest version.
Hope this helps.
Regards